We collected polychaete diversity and abundance data at a range of impacted and reference sites near an alumina refinery in Melville Bay, northern Australia. The aims were to measure the impact of sediment modified by the alumina refinery discharge on polychaete communities and secondly to gather baseline data from which to measure future changes. Polychaete communities in both soft-bottom habitats and subtidal areas adjacent to mangrove forests were studied. We also developed and deployed an artificial substratum device to sample polychaetes associated with hard-substrate habitats. For each habitat, polychaete community composition was different between impacted and reference sites and at multiple time points. The impact of future changes either from bioremediation or management practices can be measured against these baseline data. Indicator species analysis was used to identify polychaete species that were significantly different at the locations tested, and we discuss their potential as indicator species.